Analysis of the algorithm: From rankings to backup genes.

Ranking section

For each of the affected genes present in the list, a ranking with the score and percentile of every possible gene was obtained. Once this was done, the position for every known backup gene was obtained and the statistical descriptor of all the values calculated.

Table 1. Performance summary for every kernel and net before integration.

Net Kernel tpr_down_ci_0.95 tpr_up_ci_0.95 fpr_down_ci_0.95 fpr_up_ci_0.95 f
biological_process ct 0.0778064738292011 0.111570247933884 0.000950606006713253 0.00168636368202033 0.0818546078992559
biological_process el 0.0695592286501377 0.0991735537190083 0.00072788458072891 0.00134789447158093 0.0823798627002288
biological_process ka 0.0957960027567195 0.128876636802205 0.000771045818133691 0.00145235613663785 0.102959309494451
biological_process node2vec 0.0640495867768595 0.0964187327823691 0.000670010688501382 0.00121775945613313 0.0825998645903859
biological_process rf 0.0771349862258953 0.112276170798898 0.000967223701648416 0.00167210939258706 0.0829493087557604
cellular_component ct 0.00598802395209581 0.0838323353293413 0.00040730920359071 0.00344216209309012 0.075
cellular_component el 0.0662650602409639 0.174698795180723 0.00024757812687181 0.00235598540087691 0.173228346456693
cellular_component ka 0.114457831325301 0.240963855421687 0.00043106546444858 0.00351600872113918 0.210884353741497
cellular_component node2vec 0.108433734939759 0.228915662650602 0.00102225807224489 0.0082020237515274 0.140515222482436
cellular_component rf 0.132530120481928 0.271234939759036 0.000910248935813374 0.00606187057254438 0.201117318435754
disease ct 0.266718506998445 0.326594090202177 0.00205927074854082 0.00268213605723295 0.162407254740313
disease el 0.258942457231726 0.327371695178849 0.00160645271333739 0.00200385371150275 0.191452991452991
disease ka 0.286936236391913 0.342923794712286 0.00145673830955329 0.00194011631857533 0.206549118387909
disease node2vec 0.283048211508554 0.349144634525661 0.00103033740429857 0.00143319863601632 0.249925969795677
disease rf 0.236391912908243 0.296267496111975 0.00174028910463264 0.00222500183741193 0.162534435261708
genetic_interaction_weighted ct 0.0197278911564626 0.036734693877551 0.00174297535240062 0.00509262125782431 0.0162350212601469
genetic_interaction_weighted el 0.00340136054421769 0.0136054421768707 0.00397478755493665 0.0136685792758293 0.00209289221605087
genetic_interaction_weighted ka 0.0272108843537415 0.0462585034013605 0.000403452860210331 0.00145744206096829 0.040510127531883
genetic_interaction_weighted node2vec 0.0197278911564626 0.0374149659863946 0.000530937421873722 0.00140682791540983 0.0302710313269975
genetic_interaction_weighted rf 0.019047619047619 0.0374149659863946 0.000317762206391226 0.000894582388029711 0.0392506690454951
molecular_function ct 0.0369458128078818 0.0862068965517241 0.000636337688697197 0.00190917163516428 0.0597014925373134
molecular_function el 0.0812807881773399 0.152709359605911 0.000420736606198994 0.00183638843080046 0.135869565217391
molecular_function ka 0.0886083743842365 0.152709359605911 0.000232567973275826 0.00106648272654235 0.16260162601626
molecular_function node2vec 0.0541871921182266 0.110837438423645 0.000439553469491311 0.00167919362340902 0.0916230366492147
molecular_function rf 0.0738916256157636 0.142857142857143 0.000507421032601801 0.00153479005454776 0.121761658031088
pathway ct 0.11018711018711 0.170530145530145 0.000996892340713388 0.00242655548265356 0.136105860113422
pathway el 0.160416666666667 0.24796875 0.000689112793503941 0.00164544037352851 0.221748400852878
pathway ka 0.158333333333333 0.22921875 0.000452669350470344 0.00115983805626833 0.22488038277512
pathway node2vec 0.06875 0.145833333333333 0.00121044547241642 0.00235750452033579 0.109952606635071
pathway rf 0.13125 0.23125 0.00072477957800027 0.00159203556251796 0.217002237136465
phenotype ct 0.157718120805369 0.213926174496644 0.000792937453713055 0.00129124681134376 0.17397825271841
phenotype el 0.204697986577181 0.276845637583893 0.000754056419578536 0.00112287454087091 0.238095238095238
phenotype ka 0.28185822147651 0.347315436241611 0.000837840466198374 0.00119693365350808 0.274607703281027
phenotype node2vec 0.124056999161777 0.179379715004191 0.000862452675069515 0.00140338383071421 0.141859610437339
phenotype rf 0.236556208053691 0.302852348993289 0.00110933444047966 0.00159277587019457 0.219053791315619
protein_interaction ct 0.147339699863574 0.189631650750341 0.00144187276915974 0.00203551357077403 0.110323438192291
protein_interaction el 0.0811732605729877 0.111203956343793 0.00174833133734406 0.00260806172645651 0.0558375634517766
protein_interaction ka 0.162457337883959 0.204095563139932 0.000846005025905856 0.00125682800773631 0.161712247324614
protein_interaction rf 0.148703956343793 0.188949522510232 0.0014535176674346 0.00202490865712498 0.1105216622458

Table 2. Performance summary for every kernel after integration

Integration Kernel tpr_down_ci_0.95 tpr_up_ci_0.95 fpr_down_ci_0.95 fpr_up_ci_0.95 f
integration_mean_by_presence ct 0.138024357239513 0.177266576454668 0.000632031651691954 0.00101796094083609 0.159327731092437
integration_mean_by_presence el 0.303317535545024 0.367654028436019 0.00050951757922795 0.000732656649059165 0.346414073071719
integration_mean_by_presence ka 0.3385240352065 0.398104265402844 0.000532161191144038 0.000743666179419905 0.366021646441456
integration_mean_by_presence node2vec 0.0737982396750169 0.102911306702776 0.000124329261065885 0.000459742301462437 0.134282807731434
integration_mean_by_presence rf 0.274187542315504 0.327691266079892 0.000917945011607938 0.00139726626679897 0.244654939106901
mean ct 0.10893098782138 0.155615696887686 0.00041017060424637 0.000684406835789419 0.170961145194274
mean el 0.327691266079892 0.393364928909953 0.000575168076893581 0.000844218921751578 0.35702693930542
mean ka 0.316858496953284 0.40624576844956 0.000470011085057482 0.000650128744692767 0.392156862745098
mean node2vec 0.180771834800271 0.239675016926202 0.000569939276194549 0.000918003109393482 0.230362803804156
mean rf 0.199035206499661 0.262728503723764 0.00067856761071695 0.000933660462597808 0.23514043109079

Backup Pairs Coverage By Layer

Backup Pairs Coverage By Layer

Backup Pairs Coverage By Layer

CDF plots of non integrated kernels

ROC plots of integrated kernels

ROC plots of integrated kernels

CDF plots of integrated kernels